He was the superintendent for the southern district of the British Indian Department from 1761 to 1779. His northern counterpart was Sir William Johnson, based in the colony of New New York Born in Inverness, Scotland in 1718, by 1748 Stuart had immigrated to the British colony of South Carolina.
There he worked as a merchant and became prominent in local affairs
In 1760 he served as a militia captain in the Anglo-Cherokee War (1759–1761). Stuart was captured by the Cherokee, but he was ransomed by Chief Attakullakulla and returned to South Carolina.
Captain Stuart"s familiarity with Native Americans and the frontier earned his appointment in 1761 as royal superintendent in the Indian Department. His role was to help Great Britain and the colonies bring order to their relations with the Southeast Indians (who became known as the "Five Civilized Tribes").
He was also prevent the recurrence of anti-British native confederations, such as the one that organized Pontiac"s Rebellion in 1763.
Stuart appointed as his deputy in 1762 Alexander Cameron, who had served at Fort Prince George during the Anglo-Cherokee War. He had long experience with and empathy for the Cherokee, who called him "Scotchie" and considered him one of the few white men they trusted. He helped build relations with the Southeast Indians and bring peace to the backcountry in the years before the American Revolutionary War.
When the war broke out in 1775, most Native American leaders in Stuart and Cameron"s area supported the British.
In the summer of 1776, partly under their direction, the Cherokee opened a series of concerted attacks against frontier settlements from Tennessee to central South Carolina. Williamson gathered reinforcements, however, and led several expeditions against the Cherokee, killing an estimated 2,000 and destroying half of their 62 towns.
During the war Stuart fled to Georgia and then to Pensacola in the Loyalist colony of West Florida. He died there in 1779.